INSILICO IDENTIFICATION OF PROTEIN-PROTEIN INTERACTIONS AND STRUCTURE-BASED FUNCTIONAL ANNOTATION OF CAJANUS CAJAN TRYPSIN INHIBITOR BY TARGETING INTEGRIN š¼VĪ²III
Year: 2024
Type: article
Abstract: In this insilico work, we aim to explore the anti-angiogenic potential of Cajanus cajan trypsin inhibitors with pro-cancerous integrin š¼VĪ²III receptor based on protein-protein interaction approach. The study design was optimized to predict the best lead trypsin inhibitor molecule from a list of 12 proteins from Cajanus cajan (CcTI-1 to CcTI-12) retrieved via NCBI database and structured using C-I-TASSER, Alpha fold, Raptor X, and Tr-Rosetta servers. The best ranked 3D-structures from Alpha Fold with C-score -1.1- to -1.36 were validated using ramachandran plot >90% favored region, errat ~80%, and verify3D with ~86% score. Docking of CcTIs against integrin š¼VĪ²III (PDB ID: 3IJE) was carried out by ClusPro, PatchDock, ZDock, HDOCK, and HADDOCK servers. The highest negative ĪiG and better interface interaction by PDBePISA suggested CcTI-11 x integrin š¼VĪ²III from PatchDock and CcTI-9 x integrin š¼VĪ²III from ZDock with ĪiG of -6.9 and -16.7 and interface energies of 2634.4 and 1735.9 as best two docked complexes. Docking stability analysis of CcTI-9 and CcTI-11 docked structures by simulations at 100ns resulted in rmsd, rmsf, and gyration values to be 0.833nm and 0.342nm, 0.186nm and 0.126nm, 4.2nm and 4.1nm. Conclusively, better structural stability, less fluctuation, high compactness, and a higher hydrogen bonding, predicted CcTI-11 protein (accession no. >trIAOA151QRM2) to have a stronger binding with integrin š¼VĪ²III, a possible down-regulator of the receptor.
Authors: UNZILA YASIN, ALEENA SUMRIN
Institution: University of the Punjab
Language: English
Subfield: Computational Theory and Mathematics
Field: Computer Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W6949501016
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